hERGBoost: A gradient boosting model for quantitative IC prediction of hERG channel blockers.

The human ether-a-go-go-related gene (hERG) potassium channel is pivotal in drug discovery due to its susceptibility to blockage by drug candidate molecules, which can cause severe cardiotoxic effects. Consequently, identifying and excluding potential hERG channel blockers at the earliest stages of drug development is crucial. Most traditional machine learning models predict a molecule's cardiotoxicity or non-cardiotoxicity typically at 10 μM, which doesn't account for compounds with low IC values that are non-toxic at therapeutic levels due to their high effectiveness at lower concentrations.

Enhanced anticancer efficacy of photodynamic therapy in combination with immunotherapy.

Photodynamic therapy (PDT) is known to trigger immunogenic cell death (ICD), leading to an anticancer effect even in untreated metastatic cancer, a phenomenon called the "abscopal effect". Furthermore, ICD induction activates an immune response, which may synergize with immunotherapy. The objective of our research was to evaluate the anticancer efficacy of combining PDT with immunotherapy.

Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression.

Synthetic sRNAs show promise as tools for targeted and programmable gene expression manipulation. However, the design of high-efficiency synthetic sRNAs is a challenging task that necessitates careful consideration of multiple factors. Therefore, this study aims to investigate rational design strategies that significantly and robustly enhance the efficiency of synthetic sRNAs.

Engineered T Cell Receptor for Cancer Immunotherapy.

Among the therapeutic strategies in cancer immunotherapy-such as immune-modulating antibodies, cancer vaccines, or adoptive T cell transfer-T cells have been an attractive target due to their cytotoxicity toward tumor cells and the tumor antigen-specific binding of their receptors. Leveraging the unique properties of T cells, chimeric antigen receptor-T cells and T cell receptor (TCR)-T cells were developed through genetic modification of their receptors, enhancing the specificity and effectiveness of T cell therapy. Adoptive cell transfer of chimeric antigen receptor-T cells has been successful for the treatment of hematological malignancies.

Nakai Alleviates Cognitive Decline in Alzheimer's Disease by Reducing β-Amyloid and Neuroinflammation.

Recently, natural herbs have gained increasing attention owing to their comparatively low toxicity levels and the abundance of historical medical documentation regarding their use. Nevertheless, owing to a lack of knowledge regarding these herbs and their compounds, attempts to find those that could be beneficial for treating diseases have often been ; thus, there is now a growing demand for an method to identify beneficial herbs. In this study, we present a computational approach for identifying natural herbs specifically effective in treating cognitive decline in Alzheimer's disease (AD) sufferers, which analyzes the similarities between herbal compounds and known drugs targeting AD-related proteins.

A machine learning-based quantitative model (LogBB_Pred) to predict the blood-brain barrier permeability (logBB value) of drug compounds.

Motivation: Efficient assessment of the blood-brain barrier (BBB) penetration ability of a drug compound is one of the major hurdles in central nervous system drug discovery since experimental methods are costly and time-consuming. To advance and elevate the success rate of neurotherapeutic drug discovery, it is essential to develop an accurate computational quantitative model to determine the absolute logBB value (a logarithmic ratio of the concentration of a drug in the brain to its concentration in the blood) of a drug candidate.

Results: Here, we developed a quantitative model (LogBB_Pred) capable of predicting a logBB value of a query compound.

Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology.

In microbial biotechnology, there is a constant demand for functional peptides to give new functionality to engineered proteins to address problems such as direct delivery of functional proteins into bacterial cells, enhanced protein solubility during the expression of recombinant proteins, and efficient protein secretion from bacteria. To tackle these critical issues, we selected three types of functional small peptides: cell-penetrating peptides (CPPs) enable the delivery of diverse cargoes into bacterial cytoplasm for a variety of purposes, protein-solubilizing peptide tags demonstrate remarkable efficiency in solubilizing recombinant proteins without folding interference, and signal peptides play a key role in enabling the secretion of recombinant proteins from bacterial cells. In this review, we introduced these three functional small peptides that offer effective solutions to address emerging problems in microbial biotechnology.

Direct measurements of the colloidal Debye force.

Colloids often behave in a manner similar to their counterparts in molecular space and are used as model systems to understand molecular behavior. Here, we study like-charged colloidal attractions between a permanent dipole on an interfacial particle and its induced dipole on a water-immersed particle caused by diffuse layer polarization. We find that the scaling behavior of the measured dipole-induced dipole (D‒I) interaction via optical laser tweezers is in good agreement with that predicted from the molecular Debye interaction.

Effects of rosiglitazone, an antidiabetic drug, on Kv3.1 channels.

Rosiglitazone is a thiazolidinedione-class antidiabetic drug that reduces blood glucose and glycated hemoglobin levels. We here investigated the interaction of rosiglitazone with Kv3.1 expressed in Chinese hamster ovary cells using the whole-cell patch-clamp technique.

Retardation of Capillary Force between Janus Particles at the Oil-Water Interface.

Interactions among colloidal particles govern the hierarchical microstructure and its physical properties. Here, optical laser tweezers and Monte Carlo simulations are used to evaluate the effects of azimuthal rotation of Janus particles at the oil-water interface on interparticle interactions. We find that the capillary-induced attractive force between two Janus particles at the interface can be relaxed by azimuthal rotation around the critical separation region, at which the capillary force is ∼0.

Inflammatory Cytokine: An Attractive Target for Cancer Treatment.

The relationship between inflammation and cancer has attracted attention for a long time. The inflammatory tumor microenvironment consists of inflammatory cells, chemokines, cytokines, and signaling pathways. Among them, inflammatory cytokines play an especially pivotal role in cancer development, prognosis, and treatment.

Strategies for Manipulating T Cells in Cancer Immunotherapy.

T cells are attractive targets for the development of immunotherapy to treat cancer due to their biological features, capacity of cytotoxicity, and antigen-specific binding of receptors. Novel strategies that can modulate T cell functions or receptor reactivity provide effective therapies, including checkpoint inhibitor, bispecific antibody, and adoptive transfer of T cells transduced with tumor antigen-specific receptors. T cell-based therapies have presented successful pre-clinical/clinical outcomes despite their common immune-related adverse effects.

The antidiabetic drug rosiglitazone blocks Kv1.5 potassium channels in an open state.

An antidiabetic drug, rosiglitazone is a member of the drug class of thiazolidinedione. Although restrictions on use due to the possibility of heart toxicity have been removed, it is still a drug that is concerned about side effects on the heart. We here examined, using Chinese hamster ovary cells, the action of rosiglitazone on Kv1.

Role of Nitric Oxide and Protein S-Nitrosylation in Ischemia-Reperfusion Injury.

Ischemia-reperfusion injury (IRI) is a process in which damage is induced in hypoxic tissue when oxygen supply is resumed after ischemia. During IRI, restoration of reduced nitric oxide (NO) levels may alleviate reperfusion injury in ischemic organs. The protective mechanism of NO is due to anti-inflammatory effects, antioxidant effects, and the regulation of cell signaling pathways.

Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production.

Background: As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform because of its relatively fast growth.

Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review.

Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering.

Prevalence of Anemia in Pediatric Patients According to Asthma Control: Propensity Score Analysis.

Purpose: To investigate whether the degree of asthma control is associated with anemia in pediatric patients.

Patients And Methods: A cross-sectional study was performed using a dataset from the Health Insurance Reviews & Assessment Service (HIRA) of South Korea in 2016, which included children and adolescent patients diagnosed with asthma. Binary logistic regression was used to assess the association between asthma control and the prevalence of anemia.

Optimized expression of Hfq protein increases Escherichia coli growth.

Escherichia coli is a widely used platform for metabolic engineering due to its fast growth and well-established engineering techniques. However, there has been a demand for faster-growing E. coli for higher production of desired substances.

Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology.

In bacterial biotechnology, instead of producing functional proteins from plasmids, it is often necessary to deliver functional proteins directly into live cells for genetic manipulation or physiological modification. We constructed a library of cell-penetrating peptides (CPPs) capable of delivering protein cargo into bacteria and developed an efficient delivery method for CPP-conjugated proteins. We screened the library for highly efficient CPPs with no significant cytotoxicity in Escherichia coli and developed a model for predicting the penetration efficiency of a query peptide, enabling the design of new and efficient CPPs.

Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1.

Background: Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source.

Molecular cloning and functional analysis of deubiquitinase CYLD in rainbow trout, Oncorhynchus mykiss.

Deubiquitinase cylindromatosis (CYLD) inhibits MAPK and NF-κB activation pathways by deubiquitinating upstream regulatory factors. Although CYLD has been identified and actively studied in mammals, nothing is known about its putative function in fish. In this study, we identified the gene encoding CYLD (OmCYLD) from rainbow trout, Oncorhynchus mykiss, and examined its role during pathogenic infections.